The editorial, authored by Diego Ripamonti of Papa Giovanni XXIII Hospital in Bergamo, Maria Santoro and Francesca Ceccherini Silberstein of the University of Rome Tor Vergata, Joseph Fokam of CIRCB in Yaoundé, Cameroon, and Josep M. Llibre of CIBER Epidemiology and Public Health in Badalona, Spain, frames the collection around a central tension. The extensive roll-out of dolutegravir (DTG), a second-generation INSTI, across Africa has been followed by treatment-emergent resistance, largely because of the high prevalence of reverse transcriptase-associated mutations in those regions. Recent estimates place DTG-based antiretroviral therapy resistance rates in Sub-Saharan Africa between 3.9 and 19.6 percent, a range that threatens the durability of the region’s most important therapeutic advance.

Several studies in the collection deploy molecular epidemiology to map how HIV moves through populations. Gan and colleagues used molecular network technology based on HIV pol gene sequences to reveal transmission links among 1,162 men who have sex with men in Northeast China. By combining degree centrality and betweenness centrality, network measures that identify individuals with many connections or positions bridging transmission clusters, the team pinpointed people at high risk of onward transmission. Such targeting matters because undiagnosed people with HIV are the primary drivers of sustained transmission, and network analysis can direct interventions toward the individuals most likely to spread the virus.

Molecular phylogenetics also illuminated the history of epidemics in Eastern Europe and Central Europe. Kirpich and colleagues conducted the first systematic molecular epidemiology study of the HIV epidemic in Belarus, revealing two distinct epidemic waves spanning 1997 to 2005 and 2009 to 2018, each driven by different dominant modes of transmission. Reconstruction of HIV introduction routes confirmed linkages with neighboring Russia and Ukraine. In Hungary, Zsichla and colleagues analyzed partial pol sequences from 1,120 subjects collected between 2008 and 2024, finding that recent infections originate mainly from domestic transmission among men who have sex with men, with increasing introductions of non-B subtypes arriving from Eastern Europe.

Transmission risk is not determined by viral genetics alone but by virological status. He and colleagues surveyed 35,513 people with HIV in Zhejiang province, China, in 2022, categorizing sexual transmission risk across four plasma HIV RNA levels, from minimal risk among those below 50 copies per milliliter on antiretroviral therapy to high risk among those viremic off treatment. The vast majority, 88.6 percent, showed effective virological control on therapy with no transmission risk. However, people aged 16 to 24 years, men, heterosexuals and those with shorter follow-up had increased odds of being at risk, highlighting the need for more focused prevention education. Shi and colleagues tested contact tracing among 1,612 newly diagnosed people with HIV in Yunnan Province, identifying 2,226 close contacts of whom 17.8 percent tested positive for HIV, mostly newly diagnosed. Detection rates were higher among contacts identified by recently infected index cases, suggesting how tracing programs can be refined for efficiency.

Community viral load, the mean of individual plasma HIV RNA levels in a geographical area, serves as a measure of both the effectiveness of the HIV care cascade and the population’s transmission potential. Arsuffi and colleagues reported a retrospective longitudinal single-cohort study in northern Italy confirming improved virological control in the INSTI era, along with shifts in the composition of the top 10 percent of viral loads over time, increasingly including women and non-Italian individuals. Identifying subgroups with greater transmission potential allows more intensive monitoring where it is most needed. Meanwhile, Mayanja and colleagues examined peer education for oral pre-exposure prophylaxis in Uganda, implementing a randomized clinical trial with a qualitative component comparing health worker counselling alone against counselling plus monthly group peer education sessions for four months. They confirmed the negative impact of community perceptions on PrEP use as major social and cultural barriers among adolescent girls and young women, who remain major drivers of incident infections in Africa despite persistently low PrEP uptake, adherence and persistence.

Drug resistance surveillance emerged as a technical cornerstone of the collection. Monitoring transmitted drug resistance is necessary to select appropriate regimens in different settings. Lv and colleagues reported a high prevalence of the V179D/E mutation, 14.8 percent, a polymorphic NNRTI-associated mutation conferring potential low-level resistance, among antiretroviral therapy-naive people with HIV in Guangzhou. Comparing people with pretreatment NNRTI resistance, unique presence of V179D/E and a no-resistance group, the team found this mutation may impair early virological response within the first year of therapy. Ouro-Medeli and colleagues used next-generation sequencing to assess transmitted resistance in 316 treatment-naive subjects in Togo in 2023. Although resistance to first-generation INSTIs was found in 17.2 percent of samples, no resistance mutations to dolutegravir or to protease inhibitors were detected, and mutations were found in only 0.6 percent and 6.3 percent for NRTIs and NNRTIs respectively. These findings confirm low levels of DTG resistance and support the ongoing systematic switch in the region.

The picture darkens in real-world treatment settings. Mac Asaga and colleagues reported a cross-sectional multicenter cohort of 412 subjects in tertiary care in Nigeria, mostly on NNRTI-based regimens. Alongside a high burden of advanced HIV disease, 38 percent with CD4 counts below 200 cells per milliliter, only 26.9 percent had viral loads below 1,000 copies per milliliter and just 10.4 percent below 40 copies per milliliter, with 86 percent of viremic subjects harboring drug-resistant HIV-1. Although tertiary care concentrates individuals with resistant virus and adherence issues, the findings confirm the need for genotyping at failure and for newer drugs in real life. Zewdu and colleagues studied 359 young children and adolescents in Ethiopia since the 2019 introduction of DTG-based regimens, finding that children below 10 years of age, particularly those without parents and with opportunistic infections, were at higher risk of virological failure. Zheng and colleagues analyzed persistent low-level viremia in 9,649 people with HIV on INSTI-sparing regimens in Guizhou Province from 2016 to 2022, finding virological failure rates ranging from 6.1 to 13.7 percent depending on the low-level viremia threshold, and highlighting the need for intensified detection and monitoring among middle-aged and older adults.

Simplification to single tablet regimens has expanded rapidly, reducing drug interactions and toxicity while enhancing adherence. Mengato and colleagues reported the multicenter retrospective observational MOSAICO study in 490 people with HIV on stable therapy across 20 Italian centers who switched to single tablet versus multi-tablet regimens between 2017 and 2019. At week 48, real-world effectiveness confirmed the durability of single tablet regimens, with INSTI-based regimens predominant among dual therapies. Yet Appiedu-Addo and colleagues reviewed persistent gaps that prevent developing regions from managing HIV as a chronic disease as western countries do, pointing to a double standard in virological suppression thresholds, with the World Health Organization accepting below 1,000 copies per milliliter versus below 50 copies per milliliter in western countries, and in access to newer antiviral classes including long-acting options for both treatment and prophylaxis.

Beyond virological control, the collection addresses comorbidities reshaping the lives of people with HIV. Hu and colleagues explored predictors of metabolic dysfunction-associated steatotic liver disease in 814 people with HIV on stable therapy at a Chinese tertiary care center between 2018 and 2025, finding the condition in 14 percent over a median follow-up of 2.8 years, driven largely by the lymphocyte-to-HDL cholesterol ratio rather than systemic inflammation markers. Huang and colleagues analyzed the global burden of syphilis among women of childbearing age from 1990 to 2021 using the Global Burden of Disease 2021 database, with the burden remaining significant in low- and middle-income countries where syphilis in pregnancy is associated with preventable maternal and child adverse events. The editorial concludes that stopping the HIV epidemic where the disease burden is highest will require more intensive virological monitoring in key subgroups, early genotyping at failure, and extended availability of modern antiretroviral classes and long-acting options for both therapy and prophylaxis. As long as these gaps persist, the editors warn, the 95-95-95 UNAIDS targets for 2030 will remain out of reach.

Subject of Research: Editorial: Towards control of the HIV epidemic: trends in epidemiology and emerging drug resistance in the integrase inhibitor era

Article Title: Editorial: Towards control of the HIV epidemic: trends in epidemiology and emerging drug resistance in the integrase inhibitor era

Article References: Ripamonti, D., Santoro, M., Fokam, J., Ceccherini Silberstein, F., & Llibre, J. M. (2026). Editorial: Towards control of the HIV epidemic: trends in epidemiology and emerging drug resistance in the integrase inhibitor era. Frontiers in Epidemiology, 6, Article 1991472. https://doi.org/10.3389/fepid.2026.1991472

Image Credits: AI Generated

DOI: 10.3389/fepid.2026.1991472

Keywords: Editorial, Towards, control, epidemic, trends, epidemiology, emerging, drug, resistance, integrase, inhibitor, scientific research

Integrons are genetic platforms that bacteria use to capture, stockpile and rearrange small mobile elements called gene cassettes. Each cassette typically carries a single gene and its own recombination site, and the cassettes sit in arrays that can be shuffled by an integrase enzyme in response to stress. This architecture is famously responsible for the rapid spread of antibiotic resistance genes among pathogens, but the same machinery also represents an evolutionary archive of functions that bacteria have recruited over millions of years, from metabolic enzymes to toxins and defensive systems. Until now, most efforts to mine this archive have relied on laborious one-cassette-at-a-time approaches or on sequence-based predictions that say little about what a gene actually does.

The new study, led by Filipa Trigo da Roza and José Antonio Escudero of the Universidad Complutense de Madrid, together with colleagues including Melanie Blokesch of the École Polytechnique Fédérale de Lausanne, introduces two tools with evocative names: the cassette gatherer and the cassette hunter. Both exploit a clever piece of molecular engineering in which a class 1 integron recombination site, known as attI1, is embedded inside a gene that acts as a counterselection marker. In the plasmid-based version, the attI1 site was inserted into the ccdB toxin gene from Vibrio fischeri; in the chromosomal version, it was placed inside the sacB gene from Bacillus subtilis.

The logic of the system is elegantly simple. In its empty state, the disrupted toxin gene kills or prevents growth of the host bacterium under selective conditions. But when the integrase catalyses the capture of a gene cassette at the embedded attI1 site, the cassette restores the reading frame of the marker, inactivating the counterselection and allowing the cell to survive. Only cells that have successfully captured a cassette form colonies, which means the selection is entirely independent of the sequence or predicted function of the captured gene. This sequence- and function-independence is what distinguishes the approach from earlier methods that depended on PCR primers or prior knowledge of cassette boundaries.

The researchers deployed the plasmid-based cassette gatherer and the chromosomal cassette hunter in a naturally competent strain of Vibrio cholerae from which the native superintegron had been removed. Taking advantage of the bacterium’s ability to take up DNA from its environment, a capacity triggered by growth on chitin, the team could deliver genomic libraries directly into cells where the engineered integron machinery awaited them. When applied to a panel of Vibrio species, including V. cholerae, V. vulnificus, V. mimicus and V. parahaemolyticus, the tools recovered hundreds of single cassettes per assay with more than 99 percent specificity, a capture rate that dwarfs what conventional cloning strategies could achieve.

High-throughput sequencing of the resulting libraries confirmed that the recovered cassettes faithfully represented the diversity of the source integrons. Correlation analyses showed that the abundance of each cassette in the recovered pools tracked reproducibly with its representation in the starting material, and that the same cassette repertoires were recovered by both the plasmid-based and chromosomal versions of the tool. The data also revealed the diversity of functions hidden in these arrays, with many cassettes encoding proteins of unknown function, a reminder of how much uncharacterised biology remains buried in bacterial genomes.

To demonstrate the discovery power of the approach, the researchers turned their cassette libraries against two very different bacteriophages: ICP2, a vibriophage that preys on pandemic V. cholerae, and the classic Escherichia coli phage T4. Screens of the recovered cassettes identified nine distinct phage-defence systems, five of which had never been described before. The result builds on a series of recent studies showing that mobile integrons and sedentary chromosomal integrons act as biobanks of anti-phage defence, and it provides the first general-purpose pipeline for converting that observation into a systematic, high-throughput inventory of defence genes.

The significance of the advance extends well beyond phage defence. Because integron cassettes are exchanged across bacterial lineages through horizontal gene transfer, they constitute a naturally curated collection of genes that have passed repeated tests of utility in diverse cellular contexts. Gene cassette PCR, developed two decades ago, allowed researchers to amplify cassette boundaries from environmental DNA, but the products were mixtures that resisted clean isolation. Bioinformatic surveys, including comprehensive scans of metagenomes, have catalogued millions of predicted cassettes, yet prediction alone cannot assign function. The gatherer and hunter tools close this gap by pairing unbiased physical recovery of individual cassettes with immediate amenability to functional screens, whether for antibiotic resistance, metabolic activities, antimicrobial compounds or industrial enzymes.

The technical groundwork for the study drew on decades of integron biology, from the discovery of the distinctive V. cholerae superintegron in 1998 to detailed dissections of how attC recombination sites fold into single-stranded hairpins that guide strand selection during recombination. The team also engineered the recipient strain to optimise natural transformation, deleting extracellular nucleases and tuning competence regulators so that incoming genomic DNA could recombine efficiently into the capture platform. Structural predictions generated with AlphaFold3 guided the placement of the attI1 site inside the counterselection markers, minimising disruption of protein folding while preserving the lethal phenotype needed for stringent selection.

The tools, their datasets and the analysis scripts have been made available through Zenodo and GitHub, and the underlying strains are covered by patent filings, signalling likely commercial interest in what amounts to a programmable gene-discovery platform. As sequencing continues to reveal integron cassettes in environments ranging from soil and ocean to the human gut, the ability to recover and test those genes at scale transforms a passive cataloguing exercise into an active search for function. For a field that has spent forty years documenting integrons as agents of bacterial evolution, the new work offers something rarer: a way to read, one cassette at a time, the full library of tricks that bacteria have been collecting all along.

The choice of Vibrio cholerae as the engineering chassis reflects the deep historical connection between integron research and this organism. The massive superintegron of V. cholerae, first described in 1998, carries well over a hundred cassettes and remains the archetype of the sedentary chromosomal integrons found across Vibrionaceae. Because the integrase of class 1 integrons and the V. cholerae superintegron integrase share overlapping recombination specificities at attC sites, the engineered platform can in principle process cassettes arriving from a wide range of donor integrons, which is precisely what the cross-species recovery experiments demonstrated.

The phage-defence findings also fit into a rapidly consolidating picture. Within the past two years, independent teams have reported that mobile integrons in clinical settings encode anti-phage systems, that sedentary chromosomal integrons function as biobanks of defence genes, and that V. parahaemolyticus integrons are particularly rich in such systems. The nine systems identified here, five of them entirely new, suggest that this enrichment is not a peculiarity of any single lineage but a general property of integron arrays, plausibly reflecting the intense phage pressure experienced by bacteria in aquatic environments where cassettes are most actively exchanged.

Another dimension worth noting concerns expression. Cassette arrays are transcribed from a single promoter positioned in the integrase gene region, and the translation rate of upstream cassettes shapes the expression of those downstream, meaning that a captured gene’s activity depends heavily on its position in the array. By recovering cassettes as individual entities, the new tools sidestep this positional context entirely, allowing each gene to be assayed under standardised conditions. This decoupling of capture from native expression is likely to be important for screens targeting enzymatic or antimicrobial activities that may be silent or weakly expressed in the donor organism.

The environmental dimension is equally significant. Most integron cassettes on Earth reside in so-called environmental integrons, which are not associated with mobile elements or clinical resistance and remain almost entirely uncharacterised. Extending the gatherer and hunter workflow to metagenomic DNA from sediments, biofilms or wastewater could grant functional access to this reservoir, complementing sequence-similarity approaches that struggle with the high proportion of novel genes. As antimicrobial resistance continues to mobilise cassettes into pathogens, understanding what these elements normally do in their native hosts may prove as consequential as the biotechnological applications that motivated the work.

Subject of Research: High-throughput recovery of integron gene cassettes for functional gene discovery and phage-defence screening.

Article Title: High-throughput recovery of integron cassettes for gene discovery screens

Article References: Trigo da Roza, F., Carvalho, A., Prieto, A., Blanco, P., Vergara, E., López-Igual, R., Redrejo-Rodríguez, M., Blokesch, M., & Escudero, J. A. (2026). High-throughput recovery of integron cassettes for gene discovery screens. Nature Microbiology. https://doi.org/10.1038/s41564-026-02474-5

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02474-5

Keywords: integrons, gene cassettes, phage defence, antibiotic resistance, Vibrio cholerae, horizontal gene transfer, natural transformation, gene discovery, integrase, biotechnology, microbiology, bacterial evolution